private void AddRetentionTimeAnnotation(MSGraphPane graphPane, Graphics g, GraphObjList annotations,
PointF ptTop, string title, GraphObjType graphObjType, Color color, ScaledRetentionTime retentionTime)
{
string label = string.Format("{0}\n{1:F01}", title, retentionTime.DisplayTime); // Not L10N
FontSpec fontLabel = CreateFontSpec(color, _fontSpec.Size);
SizeF sizeLabel = fontLabel.MeasureString(g, label, graphPane.CalcScaleFactor());
PointF realTopPoint = ptTop;
ptTop = new PointF(0, ptTop.Y + sizeLabel.Height + 15);
float chartHeightWithLabel = graphPane.Chart.Rect.Height + sizeLabel.Height + 15;
double intensityChartFraction = (ptTop.Y - realTopPoint.Y) / chartHeightWithLabel;
LineObj stick = new LineObj(color, retentionTime.DisplayTime, intensityChartFraction, retentionTime.DisplayTime, 1)
{
IsClippedToChartRect = true,
Location = { CoordinateFrame = CoordType.XScaleYChartFraction },
ZOrder = ZOrder.E_BehindCurves,
Line = { Width = 1 },
Tag = new GraphObjTag(this, graphObjType, retentionTime),
};
annotations.Add(stick);
ptTop = new PointF(0, ptTop.Y - 5);
intensityChartFraction = (ptTop.Y - realTopPoint.Y) / chartHeightWithLabel;
TextObj text = new TextObj(label, retentionTime.DisplayTime, intensityChartFraction,
CoordType.XScaleYChartFraction, AlignH.Center, AlignV.Bottom)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.E_BehindCurves,
FontSpec = CreateFontSpec(color, _fontSpec.Size),
Tag = new GraphObjTag(this, graphObjType, retentionTime),
};
annotations.Add(text);
}
public GraphObjTag(ChromGraphItem chromGraphItem, GraphObjType graphObjType, ScaledRetentionTime retentionTime)
{
ChromGraphItem = chromGraphItem;
GraphObjType = graphObjType;
RetentionTime = retentionTime;
}
public override void AddPreCurveAnnotations(MSGraphPane graphPane, Graphics g,
MSPointList pointList, GraphObjList annotations)
{
if (Chromatogram == null)
return;
// Give priority to showing the best peak text object above all other annotations
if (DragInfo != null || (!HideBest && TransitionChromInfo != null) || CurveAnnotation != null)
{
// Show text and arrow for the best peak
double intensityBest = 0;
if (_bestPeakTimeIndex != -1)
{
ScaledRetentionTime timeBest = new ScaledRetentionTime(_measuredTimes[_bestPeakTimeIndex], _displayTimes[_bestPeakTimeIndex]);
float xBest = graphPane.XAxis.Scale.Transform(timeBest.DisplayTime);
intensityBest = _intensities[_bestPeakTimeIndex];
float yBest = graphPane.YAxis.Scale.Transform(intensityBest);
if (GraphChromatogram.ShowRT != ShowRTChrom.none || DragInfo != null)
{
// Best peak gets its own label to avoid curve overlap detection
double intensityLabel = graphPane.YAxis.Scale.ReverseTransform(yBest - 5);
float? massError = Settings.Default.ShowMassError && TransitionChromInfo != null
? TransitionChromInfo.MassError
: null;
double dotProduct = _dotProducts != null ? _bestProduct : 0;
TextObj text;
if (CurveAnnotation != null)
{
// Darken peptide name a little so light colors stand out against the white background.
var color = FontSpec.FontColor;
if (!GraphInfo.IsSelected)
color = Color.FromArgb(color.R*7/10, color.G*7/10, color.B*7/10);
var fontSpec = new FontSpec(FontSpec) { FontColor = color, Angle = 90 };
if (GraphInfo.IsSelected)
fontSpec = new FontSpec(fontSpec) {IsBold = true, Size = fontSpec.Size + 2, IsAntiAlias = true};
// Display peptide name label using vertical text.
text = new TextObj(CurveAnnotation, timeBest.DisplayTime, intensityLabel,
CoordType.AxisXYScale, AlignH.Left, AlignV.Center)
{
ZOrder = ZOrder.A_InFront,
IsClippedToChartRect = true,
FontSpec = fontSpec,
Tag = new GraphObjTag(this, GraphObjType.best_peak, timeBest),
};
}
else
{
string label = FormatTimeLabel(timeBest.DisplayTime, massError, dotProduct);
text = new TextObj(label, timeBest.DisplayTime, intensityLabel,
CoordType.AxisXYScale, AlignH.Center, AlignV.Bottom)
{
ZOrder = ZOrder.A_InFront,
IsClippedToChartRect = true,
FontSpec = FontSpec,
Tag = new GraphObjTag(this, GraphObjType.best_peak, timeBest),
};
}
annotations.Add(text);
}
// If showing multiple peptides, skip the best peak arrow indicator.
if (CurveAnnotation == null)
{
// Show the best peak arrow indicator
double timeArrow = graphPane.XAxis.Scale.ReverseTransform(xBest - 4);
double intensityArrow = graphPane.YAxis.Scale.ReverseTransform(yBest - 2);
ArrowObj arrow = new ArrowObj(COLOR_BEST_PEAK, 12f,
timeArrow, intensityArrow, timeArrow, intensityArrow)
{
Location = {CoordinateFrame = CoordType.AxisXYScale},
IsArrowHead = true,
IsClippedToChartRect = true,
ZOrder = ZOrder.A_InFront
};
annotations.Add(arrow);
}
}
// Show the best peak boundary lines
if (CurveAnnotation == null)
{
double startTime = 0, endTime = 0;
if (DragInfo != null)
{
startTime = DragInfo.StartTime.MeasuredTime;
endTime = DragInfo.EndTime.MeasuredTime;
}
else if (TransitionChromInfo != null)
{
var tranPeakInfo = TransitionChromInfo;
startTime = tranPeakInfo.StartRetentionTime;
endTime = tranPeakInfo.EndRetentionTime;
}
AddPeakBoundaries(graphPane, annotations, true,
ScaleRetentionTime(startTime), ScaleRetentionTime(endTime), intensityBest);
}
}
}
private void AddPeakBoundaries(GraphPane graphPane, ICollection<GraphObj> annotations,
bool best, ScaledRetentionTime startTime, ScaledRetentionTime endTime, double maxIntensity)
{
// Only show boundaries for dragging when boundaries turned off
if (!Settings.Default.ShowPeakBoundaries && (!best || DragInfo == null))
return;
float xStart = graphPane.XAxis.Scale.Transform(startTime.DisplayTime);
float xEnd = graphPane.XAxis.Scale.Transform(endTime.DisplayTime);
// Hide boundaries, if they are too close together
if (xEnd - xStart <= MIN_BOUNDARY_DISPLAY_WIDTH)
{
// But not if they are currently part of a drag operation.
if (DragInfo == null)
return;
}
// Make sure the best borders are visible
if (best)
{
float yMax = graphPane.YAxis.Scale.Transform(maxIntensity);
float yZero = graphPane.YAxis.Scale.Transform(0);
if (yZero - yMax < MIN_BEST_BOUNDARY_HEIGHT)
maxIntensity = graphPane.YAxis.Scale.ReverseTransform(yZero - MIN_BEST_BOUNDARY_HEIGHT);
}
// Summary graphs show only the best peak boundaries
else if (_isSummary)
{
return;
}
Color colorBoundaries = (best ? COLOR_BOUNDARIES_BEST : COLOR_BOUNDARIES);
GraphObjType graphObjType = best ? GraphObjType.best_peak : GraphObjType.peak;
// Make sure to get maximum intensity within the peak range,
// as this is not guaranteed to be the center of the peak
LineObj stickStart = new LineObj(colorBoundaries, startTime.DisplayTime, maxIntensity, startTime.DisplayTime, 0)
{
IsClippedToChartRect = true,
Location = { CoordinateFrame = CoordType.AxisXYScale },
ZOrder = ZOrder.B_BehindLegend,
Line = { Width = 1, Style = DashStyle.Dash },
Tag = new GraphObjTag(this, graphObjType, startTime),
};
annotations.Add(stickStart);
LineObj stickEnd = new LineObj(colorBoundaries, endTime.DisplayTime, maxIntensity, endTime.DisplayTime, 0)
{
IsClippedToChartRect = true,
Location = { CoordinateFrame = CoordType.AxisXYScale },
ZOrder = ZOrder.B_BehindLegend,
Line = { Width = 1, Style = DashStyle.Dash },
Tag = new GraphObjTag(this, graphObjType, endTime),
};
annotations.Add(stickEnd);
}
/// <summary>
/// Indicates a peak has been picked at a specified retention time
/// for a specific replicate of a specific <see cref="TransitionGroupDocNode"/>.
/// </summary>
/// <param name="nodeGroup">The transition group for which the peak was picked</param>
/// <param name="nodeTran">The transition no which the time was chosen</param>
/// <param name="peakTime">The retention time at which the peak was picked</param>
public void FirePickedPeak(TransitionGroupDocNode nodeGroup, TransitionDocNode nodeTran, ScaledRetentionTime peakTime)
{
if (PickedPeak != null)
{
var filePath = FilePath;
if (filePath == null)
return;
int iGroup = _nodeGroups.IndexOfReference(nodeGroup);
var e = new PickedPeakEventArgs(_groupPaths[iGroup],
nodeTran != null ? nodeTran.Id : null,
_nameChromatogramSet,
filePath,
peakTime);
PickedPeak(this, e);
}
}
public void FirePickedSpectrum(ScaledRetentionTime retentionTime)
{
if (PickedSpectrum != null)
PickedSpectrum(this, new PickedSpectrumEventArgs(new SpectrumIdentifier(FilePath, retentionTime.MeasuredTime)));
}
public PickedPeakEventArgs(IdentityPath groupPath, Identity transitionId,
string nameSet, MsDataFileUri filePath, ScaledRetentionTime retentionTime)
: base(groupPath, nameSet, filePath)
{
TransitionId = transitionId;
RetentionTime = retentionTime;
}
private PeakBoundsDragInfo StartDrag(GraphPane graphPane, ChromGraphItem graphItem, PointF pt,
ScaledRetentionTime time, bool bothBoundaries)
{
var tranPeakInfo = graphItem.TransitionChromInfo;
var startTime = time;
var endTime = time;
if (tranPeakInfo == null)
bothBoundaries = true;
else
{
startTime = graphItem.ScaleRetentionTime(tranPeakInfo.StartRetentionTime);
endTime = graphItem.ScaleRetentionTime(tranPeakInfo.EndRetentionTime);
}
bool draggingEnd = Math.Abs(time.DisplayTime - startTime.DisplayTime) > Math.Abs(time.DisplayTime - endTime.DisplayTime);
ScaledRetentionTime anchorTime, caretTime;
if (bothBoundaries)
anchorTime = caretTime = time;
else if (draggingEnd)
{
anchorTime = startTime;
caretTime = endTime;
}
else
{
anchorTime = endTime;
caretTime = startTime;
}
var retentionMsMs = RetentionMsMs;
bool alignedTimes = false;
if (retentionMsMs == null)
{
retentionMsMs = AlignedRetentionMsMs;
alignedTimes = true;
}
var dragType = (draggingEnd ? PeakBoundsChangeType.end : PeakBoundsChangeType.start);
var changeType = bothBoundaries ? PeakBoundsChangeType.both : dragType;
var peakBoundDragInfo = new PeakBoundsDragInfo(graphPane, graphItem, retentionMsMs, alignedTimes,
pt, dragType, changeType)
{
AnchorTime = anchorTime,
CaretTime = caretTime
};
return (graphItem.DragInfo = peakBoundDragInfo);
}
private ScaledRetentionTime GetRetentionTimeOfZeroOptStep(ChromGraphItem graphItem, ScaledRetentionTime peakTime)
{
if (graphItem.OptimizationStep == 0)
{
return peakTime;
}
ChromGraphItem mainGraphItem = GraphItems.FirstOrDefault(item =>
0 == item.OptimizationStep
&& ReferenceEquals(item.TransitionNode, graphItem.TransitionNode)
&& ReferenceEquals(item.TransitionGroupNode, graphItem.TransitionGroupNode));
if (mainGraphItem == null)
{
return ScaledRetentionTime.ZERO;
}
int iPeak = graphItem.Chromatogram.IndexOfPeak(peakTime.MeasuredTime);
ChromPeak mainPeak = mainGraphItem.Chromatogram.GetPeak(iPeak);
return mainGraphItem.ScaleRetentionTime(mainPeak.RetentionTime);
}
private ChromGraphItem FindMaxPeakItem(GraphPane graphPane, ScaledRetentionTime startTime, ScaledRetentionTime endTime)
{
double maxInten = 0;
ChromGraphItem maxItem = null;
foreach (ChromGraphItem graphItemCurr in GetGraphItems(graphPane))
{
double inten = graphItemCurr.GetMaxIntensity(startTime.MeasuredTime, endTime.MeasuredTime);
if (inten > maxInten)
{
maxInten = inten;
maxItem = graphItemCurr;
}
}
return maxItem;
}
public ChangedPeakBoundsEventArgs(IdentityPath groupPath,
Transition transition,
string nameSet,
MsDataFileUri filePath,
ScaledRetentionTime startTime,
ScaledRetentionTime endTime,
PeakIdentification identified,
PeakBoundsChangeType changeType)
: base(groupPath, nameSet, filePath)
{
Transition = transition;
StartTime = startTime;
EndTime = endTime;
Identified = identified;
ChangeType = changeType;
}
